A metal-mediated base pair that discriminates between the canonical pyrimidine nucleobases.

A nucleoside analogue comprising the ligand 1-imidazo[4,5-][1,10]phenanthroline () was applied to develop a molecular beacon capable of discriminating the canonical nucleobases cytosine and thymine. The beacon is based on the formation of a stable Ag-mediated base pair between and cytosine, whereas the presence of Ag strongly destabilizes nucleic acids comprising an artificial base pair between and thymine. Metal-mediated base pair formation was investigated by temperature-dependent UV spectroscopy and CD spectroscopy and complemented by extensive DFT calculations. The molecular beacon significantly extends the application spectrum of nucleic acids with metal-mediated base pairs. It is of potential use in the detection of single-nucleotide polymorphisms.